My models need a model file in .x accompanied by D, N and S texture files in .dds format, how would i make my model opaque?
OK, I've managed to answer this myself. I was messing with blender last night, trying some other stuff when I stumbled across the answer myself. 

You don't actually need to set any alphas in blender (except to tick the alpha box when you hit new image for the UV unwrap), it's all in the editing of the textures afterwards.

For GIMP users, simply edit your UV textures as you would normally except this time right click on the texture layer you want to be opaque, select mask layer and chose white (full opaque). 

Your texture should now be opaque, to choose how opaque it make sure the texture layer is selected and use the alpha slider located between the blend drop down and the layer list (before you do all this make sure the image you are using is in a format that can have an alpha channel, like png etc).

If you want to give it a coloured tint, or maybe darken the opaque image then use the fill tool on the mask to apply a colour. 

Then just finish up the textures as you would normally, it should now be transparent in the areas you chose.